UW-MRI Reconstruction Toolbox

This is reconstruction code developed for MRI reconstructions, primarily non-cartesian data but will work with arbitrary code. It has a focus on iterative reconstructions using coil sensitvities derieved from the data (e.g. ESPIRiT ).

Highlighted Publications using this Code

Rivera-Rivera LA, Johnson KM, Turski PA, Wieben O, Schubert T. Measurement of microvascular cerebral blood volume changes over the cardiac cycle with ferumoxytol-enhanced T2* MRI. Magn Reson Med. 2019 Jun;81(6):3588–3598. PMID: 30756424 Link
Jimenez JE, Strigel RM, Johnson KM, Henze Bancroft LC, Reeder SB, Block WF. Feasibility of high spatiotemporal resolution for an abbreviated 3D radial breast MRI protocol. Magn Reson Med. 2018;80(4):1452–1466. PMCID: PMC6721961 Link
Johnson KM. Hybrid radial-cones trajectory for accelerated MRI. Magn Reson Med. 2017;77(3):1068–1081. PMCID: PMC5040626 Link
Kaiser J, Monawer A, Chaudhary R, Johnson KM, Wieben O, Kijowski R, Thelen DG. Accuracy of model-based tracking of knee kinematics and cartilage contact measured by dynamic volumetric MRI. Med Eng Phys. 2016;38(10):1131–1135. PMCID: PMC5035576 Link
Bauman G, Johnson KM, Bell LC, Velikina JV, Samsonov AA, Nagle SK, Fain SB. 3D pulmonary perfusion MRI with radial ultra-short echo time and spatial-temporal constrained reconstruction. Magn Reson Med. 2015 Feb;73(2):555–564. PMCID: PMC4156934 Link
Johnson KM, Block WF, Reeder ScottB, Samsonov A. Improved Least Squares MR Image Reconstruction Using Estimates of k-Space Data Consistency. Magn Reson Med. 2012 Jun;67(6):1600–1608. PMCID: PMC3354012 Link

Software dependencies

Blitz++ a template array library, used for 3D+ arrays Link
Armadillo a linear algebra package. It is highly recomended you install with the Intel MKL package Link
HDF5 C++ library Link. Install From source with "--enable-fortran --enable-cxx --enable-static --disable-shared"
FFTW3 with OpenMp support Link Install From source with "--enable-float --enable-threads --enable-openmp"
[Optional]Voro++ a 3D voronoi diagram package (used for sampling density estimates). Link

GE Orchestra Support

For Orchestra support, you must additionally:

Install Ochestra 1.8 or higher and set the OX_INSTALL_DIR
Compile with gcc/g++ 4.x (e.g. 4.8)

Compiling with GE Orchestra (Example with gcc 4.8)

CC=gcc-4.8 CXX=g++-4.8 FC=gfortran-4.8 cmake ../ -DCMAKE_BUILD_TYPE=Release -DENABLE_ORCHESTRA="yes" CMAKE_INSTALL_PREFIX=${HOME}/local/ CC=gcc-4.8 CXX=g++-4.8 FC=gfortran-4.8 cmake ../ -DCMAKE_BUILD_TYPE=Debug -DENABLE_ORCHESTRA="yes" -DCMAKE_INSTALL_PREFIX=${HOME}/local/

Coding style

Code is C++99 to support current coding compatibility of Vendor libraries. Style is based on 2 space indentation according to Google's style ( https://google.github.io/styleguide/cppguide.html ) but doesn't have column width limit.

Data preparation

This code can be called from external c++ programs to avoid an explicit file.

Common Options

Options should be visible by typing "uwmri_recon -h"

Simple recon using sensitivity maps from the center of k-space

uwmri_recon -f MRI_Data.h5 -pils

Simple iterative SENSE

uwmri_recon -f MRI_Data.h5 -cg -max_iter 20

Simple L1-Wavelet regularized SENSE with FISTA

uwmri_recon -f MRI_Data.h5 -fista -max_iter 100 -threshold_type fraction -thresh 0.1

Gated Local Low Rank using Time info in the header to gate the data into 10 frames

uwmri_recon -f MRI_Data.h5 -fista -max_iter 100 -gating_type time -rcframes 10 -clear_alpha_time 0.001

uwmri/mri_recon